Bioinformatics.fr

Share a resource

Viralzone

http://www.expasy.ch/viralzone/ General website dedicated to viruses containing all viral families and genera.

CoVDB

http://covdb.microbiology.hku.hk/

Description :
Coronavirus genes and genomes

HCV Database

http://hcv.lanl.gov/

Description :
The Hepatitis C Virus (HCV) sequence database is a project funded by the Division of Microbiology and Infectious Diseases of the National Institute of Allergies and Infectious Diseases (NIAID). We strive to present HCV sequences and associated data in a userfriendly way, by providing access to the central database via a web-accessible search interface and supplying a number of analysis tools. We are assisted in this effort by an editorial board, whose members serve as 'representatives' of the user community and keep us apprised of problems and issues that we might otherwise miss.

Aknowledgement :
The HCV database is deeply indebted to the HIV database, led by Dr. Bette Korber, for much of its tools, infrastructure and philosophy; the two databases continue to collaborate closely and to share software and resources.

References :
1. Kuiken C, Yusim K, Boykin L, Richardson R. The Los Alamos hepatitis C sequence database. Bioinformatics. 2004 Sep 17 [Epub ahead of print]

RNA Virus Database

http://virus.zoo.ox.ac.uk/rnavirusdb/

Description :
The RNA Virus Database

VirHostNet

http://pbildb1.univ-lyon1.fr/virhostnet

Description :
A knowledgebase of virus-host molecular interaction networks

VirusMINT

http://mint.bio.uniroma2.it/virusmint/Welcome.do

Description :
Molecular interactions between human and viral proteins

Viral Bioinformatics

http://athena.bioc.uvic.ca/

Description :
Viral Bioinformatics provides access to viral genomes and a variety of tools for comparative genomic analyses.

Poxvirus Bioinformatics Resource Center

http://www.poxvirus.org/

Description :
Includes poxvirus genomic sequences; annotation and analysis of poxvirus genes; web-based data mining and sequence analysis tools; software for analysis of complete genomes; literature resource; repository of poxvirus species and strains; discussion forum.

Genotyping - NCBI

http://www.ncbi.nih.gov/projects/genotyping/formpage.cgi

Description :
The Genotyping tool at the NCBI identifies the genotype (or subtype) of viral sequences by using a sliding window approach to BLAST analysis against reference sequences for different viral subtypes. Results are shown as a graphical output plotting the top-scoring genotype. An alignment tool is also available.

FluGenome

http://www.flugenome.org/

Description :
FluGenome is a tool for determining lineages and genotypes of influenza A viruses.

HIV Sequence Database

http://hiv-web.lanl.gov/

Description :
The HIV Sequence Database contains all published and many unpublished HIV and related SIV DNA and translated amino acid sequences. Currently, >95,000 entries are maintained and annotated. The database is fully searchable through several search tools and contains many tools for sequence analysis.

The search tools include an interface where sequences are searchable through accession number, name, sampling country, subtype, sampling year, risk factor, coreceptor usage, phenotype and more. Another search tool uses geographic subtype distributions. The search results are presented as tables covering important sequence information and the sequences can be downloaded as multiple pairwise alignments. Some examples among the many tools are: Gene Cutter that clips pre-defined coding regions from a nucleotide alignment, then codon aligns and provides translations of the cut regions, Seq-Covert that converts between different formats, Primalign that aligns your primer or sequence fragment to the complete genome alignment, the HIV/SIV Sequence Locator that finds the position of your nucleotide or protein sequence in HIV relative to a reference, RIP that performs a recombination analysis, Hypermut that can detect hypermutated sequences, SNAP that calculates synonymous and non-synonymous substitutions, PCoord that summarizes variation among sequences in ten 'dimensions' where each sequence gets a score on each of these dimensions, and HIV-BLAST that performs a BLAST search on HIV sequences. Some simple tree building interfaces are present and more advanced and versatile tree tools are currently being developed.

The database also provides alignments of all full length HIV and SIV genomes, consensus and reconstructed ancestral sequences, and reference sequences for subtyping, recombination analyses and other purposes.

In addition, the database publishes a yearly hard copy compendium with selected sequences and review articles on recent developments in HIV genetic research. These reviews and additional tutorials on sequence analysis are also available on the web site.

Subviral RNA Database

http://subviral.med.uottawa.ca/

Description :
The Subviral RNA database contains a large number of sequences and related data on viroids, viroid-like RNAs and human hepatitis delta virus (vHDV) in a customizable and user-friendly format. In addition to the sequences themselves, many entries include additional data (e.g. position and secondary structures of the self-catalytic RNAs, prediction of the most stable secondary structures, multiple sequence aligments, duplicated sequences, etc.). Moreover, links are provided to the original GenBank, EMBL and Medline records. This database is available on the World Wide Web at http://penelope.med.usherb.ca/subviral/.

DPVweb

http://www.dpvweb.net/

Description :
DPVweb provides a central source of information about viruses, viroids and satellites of plants, fungi and protozoa. Comprehensive taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences are provided. The database also holds detailed, curated, information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene (currently, n~9000). For comparative purposes, it also contains a single representative sequence of all other fully sequenced virus species with an RNA or ssDNA genome. The start and end positions of each feature (gene, non-translated region, etc) have been recorded and checked for accuracy. As far as possible, nomenclature for genes and proteins are standardised within genera and families. Sequences of features (either as DNA or amino acid sequences) can be directly downloaded from the web site in FASTA format. The sequence information can also be accessed via client software for PC computers (freely downloadable from the web site) that enable users to make an easy selection of sequences and features of a chosen virus for further analyses.

Aknowledgement :
We thank the Association of Applied Biologists for their support, in particular by funding the development of the standalone DPV program and for sponsoring the DPVweb internet site. Rothamsted Research receives grant-aided support from the Biotechnology and Biological Sciences Research Council of the United Kingdom.

HERVd - Human Endogenous Retrovirus database

http://herv.img.cas.cz/

Description :
Human endogenous retrovirus database

References :
1.Paces J, Pavlicek A, Paces V. HERVd: database of human endogenous retroviruses. Nucleic Acids Res. 2002 Jan 1;30(1):205-6.
Paces J, Pavlicek A, Zika R., Kapitonov VV, Jurka J, Paces V. HERVd: the Human Endogenous RetroViruses Database: update. Nucl. Acids. Res. 2004 32: D50

NCBI Viral genomes

http://www.ncbi.nlm.nih.gov/genomes/VIRUSES/viruses.html

Description :
The NCBI Viral Genomes Resource (http://www.ncbi.nlm.nih.gov/genomes/VIRUSES/viruses.html) provides sequence information, as well as precomputed comparative analyses and Web tools, for all viruses and viroids for which (nearly) complete genomic sequences have been established and deposited to DDBJ, EMBL, or GeneBank. The collection currently contains over 2200 reference sequences (RefSeq) and about 6,500 additional complete sequences for more than 1,500 different viral species. The reference sequences are maintained in separate records that are further curated and updated. Whenever more than one complete genome for a species is available, a pairwise global alignment of a reference sequence with each additional sequence is provided. Precomputed clusters of related proteins (VOG) from the reference sequences help navigate among viral proteomes and summarize available functional information for most major virus groups. The data are accessible via Entrez as well as from specialized Web pages offering visualization of the sequence information at various levels of detail.

Aknowledgement :
The NCBI Viral Genomes Resource is a collaborative effort between NCBI staff and many dedicated scientists worldwide.

References :
Bao Y, Federhen S, Leipe D, Pham V, Resenchuk S, Rozanov M, Tatusov R, Tatusova T. (2004) National Center for Biotechnology Information viral genomes project. J Virol. 78: 7291-7298.

Cancel